The microscopic examination and classification of tissues has improved medical treatment. For example, in the case of many tumors, a diagnosis can be made on the basis of cell morphology and staining characteristics. Even the aggressiveness of a tumor can sometimes be predicted through microscopic evaluation. However, standard staining methods such as hematoxylin-eosin (H&E) generally can reveal only a limited amount of diagnostic information.
Recent advances in molecular medicine have provided the opportunity to understand the cellular mechanisms of disease and to select appropriate treatments. The identification of molecular markers of disease, such as tumor-specific antigens, enables diagnostic and prognostic assays to be developed which rely on the use of molecular probes (e.g., antibodies and nucleic acid probes) to detect these markers. However, the development of new molecular markers of clinical importance has been impeded by the slow and tedious process of determining the expression of these markers in large numbers of clinical specimens. For example, hundreds of tissue specimens representing different stages of tumor progression must be evaluated before the biological relevance of a given marker can be confirmed. As the number of molecular probes increases, the number of tissue samples which can be evaluated in a single experiment becomes a rate-limiting factor.
Prior to 1998, methods of grouping multiple tissue specimens on a single substrate relied on manually cutting multiple paraffin-embedded tissue specimens and forming them into a composite block (see, e.g., Battifora et al., 1986, Lab. Invest. 55: 244–248; U.S. Pat. No. 4,820,504) or into “straws” or “logs” from which transverse sections could be obtained (see, e.g., Wan et al., 1987, J. Immunol. Meth. 103: 121–129; U.S. Pat. No. 4,914,022; Miller and Groothuis, 1991, A.J.C.P. 96: 228–232). In addition to requiring a high degree of manual dexterity, these methods randomly arranged samples, making it difficult to identify specimens of interest. Methods to overcome the problems of random placement by placing tissue strips in grooves within a mold have been described by Battifora and Mehta, 1990, Lab. Invest. 63: 722–724, U.S. Pat. No. 5,002,377 and Sunblad, 1993, A.J.C.P. 102: 192–193, however, these methods are also labor intensive and time consuming.
Kononen et al., 1998, Nat. Med. 4: 844–7, have recently described a technique for generating tissue arrays comprising hundreds of tumor specimens using punched samples from archival tissue blocks. While greatly increasing the throughput of methods involving the use of tissue microarrays, the technique has been limited to the evaluation of paraffin-embedded tissue specimens which are not optimal for many types of molecular analyses.